Introduction / Overview of GenGIS

Purpose

Geography has always been an important component of evolutionary and ecological theory. The advent of sequence typing approaches such as 16S ribotyping, DNA barcoding using the COX1 gene, and multi-locus sequence typing, gives us the opportunity to understand how communities of organisms interact, disperse and evolve. This sequencing revolution is tightly coupled to the development of new algorithms for assessing and comparing populations based on their genes.

Coupled with these developments is the availability of high quality, public domain digital map data. By integrating molecular data with cartography and habitat parameters, we can visualize the geographic and ecological factors that influence community composition and function.

GenGIS is designed to bring these components together into a single software package that satisfies the following criteria:

Free and Open Source

GenGIS is released under a Creative Commons Attribution - Share Alike 3.0 license, and we have made extensive use of other free packages such as wxWidgets, R, and Python. Making GenGIS freely available allows it to be downloaded and used anywhere in the world, and allows users to inspect and modify the source code.

User-Friendly Interface

Although GenGIS is built to deal with challenging scientific questions, our goal is to make the software easy to use. This is particularly important as many users will have little experience with digital map data, apart from applications such as Google Earth.

Adaptible and Extensible

The principal strength of many open-source projects lies in the ability of a loosely organized community of users to develop and enhance the software: R and BioPerl are two examples of successful open-source projects with many contributors. Since the potential applications of GenGIS are much broader than those we have in mind, we aim to make it as easy as possible to extend its capabilities by exposing the internal data structures and offering a plugin architecture.

Developer Version – building from source code

GenGIS can be compiled using Microsoft Visual C++ 2008 Express Edition. The Visual Studio solution file (GenGIS.sln) is located in the 'win32/build/msvc' directory. Please note that the built-in Python console is only available in Release builds.

Building on MacOSX

GenGIS can be compiled using the Makefile located in the 'mac/build/gcc' directory. To compile, simply run 'make' within a terminal. Development has been performed using the gcc 4.3.3 compiler.

R and GenGIS

GenGIS integrates with the R programming language to provide additional statistics and visualization tools. Calls to the R environment are made by certain GenGIS plugins (e.g., Mantel).

Manually Configuring R (Windows)

Recent versions of R (e.g., v2.14.1) use a different installation file structure that is incompatible with the Windows version of GenGIS. The issue can be resolved by means of a harmless workaround described below. If running GenGIS on MacOSX, you may skip this section. For Windows XP users, the path to the R bin directory (e.g., C:\Program Files\R\R-2.14.1\bin) needs to be set within the Windows PATH environment variable.

Manually Transferring DLLs:

Windows XP, Vista & 7

Close GenGIS.

Go to the C:\Program Files\R\R-2.xx.x\bin\i386 directory.

Copy all the files ending in .dll to the C:\Program Files\R\R-2.xx.x\bin\ directory.

Manually Setting the PATH Variable:

Windows XP Only

Close GenGIS

Go to the C:\Program Files\R\ directory (install R if this directory is missing).

Open the folder corresponding to the latest version of R (e.g., 'R-2.14.1').

Open the bin directory.

Copy the entire directory path from the folder window (e.g., 'C:\Program Files\R\R-2.14.1\bin'). This information is what you will add to the Path variable.

Version 2.1 and above: GenGIS now supports vector data, with or without an underlying raster. If a raster file is to be used, it should be loaded before any vector data. If no raster is provided, the first vector file loaded will be used to initialize the map environment, and will be listed first. The minimap boundaries and default views will be based on the dimensions of this vector, even if other vector files are added and the original vector subsequently deleted. Any number of vector files can be loaded and viewed in GenGIS; these can be added and deleted at any stage.

GenGIS currently supports a single location and sequence file during a session. Any number of tree files can be opened.

Note: The location of sequences (sequence file) and leaves (tree file) must each map to an existing location given by the location file. The leaves of a tree file can be identifiers for either locations or sequences.

Maps

GenGIS relies on the Geospatial Data Abstraction Library (GDAL) to import several digital map file formats and projections. More information, including community support and downloads, can be found at the GDAL website.

Note: The 'gdal_merge.py' script, 'gdalwarp.exe' and 'gdal_translate.exe' executables have been very useful in preparing maps compatible with GenGIS.

Supported raster formats

GenGIS supports the formats listed on the GDAL Raster Formats page. Note that not all formats have been tested at this time. The following formats have been found to work reliably:

GeoTIFF

Arc/Info ASCIIGRID

USGS DEM (and variations thereof)

Supported vector formats

We have tested GenGIS on a number of different ESRI shape files (typically ending in .shp).

Projections

If you wish to use a specific projection, you must specify it before loading your map - GenGIS is unable to render reprojections on the fly. This is particularly true if you are loading the default world map (from GTOPO30) that ships with GenGIS: the default Mercator projection stretches the polar regions, whereas Plate Carre or Robinson will provide a much less distorted world view.

To specify the projection before loading the map, right click "New Study : Study" in the Layers tab, and select Properties. Selecting the Projection tab will allow you to choose your projection.

GenGIS currently does not support projections in which a single point is displayed in multiple locations. The best example of this is the default world map, which is modified to stretch from 89.9 degrees North to 89.9 degrees South latitude. Since the poles stretch across the entire upper and lower edges of a map in a projection such as Plate Carre, GenGIS is unable to display these properly.

Typical limits on map size

Higher processor speeds and more system RAM are required to work effectively with larger maps. Typically one gigabyte of RAM permits working with maps that are 10 megabytes or slightly greater in size.

Reducing Map Size

If the map resolution of is too high for the system hardware being used, the GDAL Utilities 'gdalwarp' or 'gdal_translate' can be used to reduce the density of points in the map. Decreasing the level of detail is an acceptable tradeoff in many cases.

Location File

The location file must be provided in either tab-delimited or comma-separated formats (e.g., the .CSV files that can be exported from Microsoft Excel). The first line of the file must be a series of headers. Each subsequent line should contain a set of attributes for a single location.

The first entry of the header must be a unique location identifier with the label Site ID or Sample ID.

A vertical coordinate labelled as Latitude (decimal degrees) or Northing (Universal Transverse Mercator, UTM) must be included but can be present at any column position after the unique location identifier. Note that positive values = north and negative values = south.

A horizontal coordinate, labelled as Longitude (decimal degrees) or Easting (Universal Transverse Mercator, UTM) must be included but can be present at any column position after the unique location identifier. Note that Positive values = east and negative values = west.

The first line of the file may look something like the following:

Site ID, Latitude, Longitude

or

Site ID, Northing, Easting

depending on the coordinate system.

GenGIS provides the ability to specify many different custom column headers within the Location file, including longer descriptive site names, environmental parameters, or a time stamp. For instance, a location file header might look like this:

Each of these values must then be specified for every entity (= row in the file), even if they are called NULL or some other placeholder value.

Sequence File

The basic specification of the sequence file is even simpler, with only two required fields:

A unique location identifier that is also found in the location file

A unique sequence identifier

The first line of the file must begin with the following column headings:

Site ID, Sequence ID

Columns containing custom information can be added after the two mandatory headings. Each row of the sequence file must define a value for each of the columns identified in the header line. Note that the 'sequence file' need not contain any molecular sequence data, nor do the entities necessarily need to have a one-to-one correspondence to actual sampled sequences.

A simple sequence file might summarize the taxonomic classification of each sampled sequence:

Multiple identical sequences at a location

A count field may be specified within a Sequence File to indicate the number of times a given sequence is present at a given site. This has the benefit of significantly reducing the size of a Sequence File.

The count field can be assigned any name within the Sequence File. Multiple count fields may be specified indicating different quantitative aspects of a named sequence type such as number of sequences or total base pairs observed. The count field can then be specified in various locations within GenGIS. For example, quantitative pie charts reflecting the number of times each sequence type is observed at a location can be created through the Location Set Properties dialog:

Open the Location Set Properties dialog

Navigate to the Charts > Colour Map tab

Select "Create quantitative charts using count data in field"

Select the desired count field from the adjacent drop down menu

Tree File

Input trees should adhere to the Newick file format, with the additional constraint that leaf labels must match up exactly with either a Site ID from the location file or a Sequence ID from the sequence file.

The Environment

Overview

The graphical user interface for GenGIS consists of a collection of different interface elements. Many features of GenGIS can be accessed through the Menu.

The most commonly used features are exposed on the Toolbar.

Data loaded into GenGIS is organized into a Layer Tree, which is made explicit to the user in the panel on the left. This hierarchical structure provides a natural organization of data and allows the properties of related data items to be set easily.

Data visualizations are displayed in the 3D Viewport. Mouse navigation within this 3D environment follows a standard world-in-hand navigation model.

Alternatively, the camera position and angle can be modified using the Navigation Widget, which also provides an overview map.

The Console provides feedback to the user such as the results of statistical tests and warnings about potential problems with loaded data.

Almost all features available through the graphical user interface can be accessed within the Python Console window. This includes loading data layers, modifying camera parameters, and accessing location or sequence data.

Information about interface elements or graphical features within the Viewport is displayed on the Statusbar.

Menu Items

File Menu

New Session: Start a new instance of GenGIS.

Open Session: Open a saved GenGIS session.

Recent Sessions: Displays a menu of recent sessions.

Save: Save session to file.

Save As...: Specify a new filename and save session to file.

Export as Image...: Save Viewport contents to a PNG image file.

Exit: Exits the program.

View Menu

Panes → Side Panel: Hide/unhide the left side panel containing the Layer tree.

About: Brings up an About GenGIS dialog box which contains a link to this website and other information.

Toolbar Buttons

The main toolbar provides easy access to frequently used features.

Open Session

Open a file to restore a previous GenGIS session.

Add raster map

Add a raster map to the currently selected study.

Add vector map

Add a vector map to the currently selected study.

Add location set

Add a location set to the currently selected map.

Add sequence data

Add sequence data to the currently selected location set.

Add tree

Add a geographic tree model to the currently selected map.

Default perspective view

Move camera to its default perspective position.

Top view

Move camera to give a top-down view of the map.

Draw layout line

Draw a straight line which can be used to layout graphic elements such as a 2D tree or pie charts.

Draw layout ellipse

Draw an ellipse which can be used to layout graphic elements such as a 2D tree or pie charts.

Draw geographic axis

Draw a polyline which can be used to test the goodness-of-fit between a tree and a non-linear geographic axes (see 2D Pylogenetic Trees).

Note: GenGIS does not support loading multiple maps, location sets or sequence sets. Adding multiple trees is experimental at this time.

Navigating the Viewport

GenGIS offers three different options to navigate maps: direct mouse gestures, a navigation widget, and two predefined views.

Mouse

The map can be moved by dragging with the left mouse button.

Camera pitch is controlled by dragging with the right mouse button in vertical directions.

Map rotation is performed by dragging with the left mouse button in horizontal directions.

Camera zoom level is controlled using the mouse scroll wheel.

Navigation Widget

The navigation widget is located within the top right region of the viewport and provides additional controls to navigate the map.

The arrows at the top of the widget move the map transversely while the 'plus' and 'minus' buttons control camera zoom.

Clicking within the overview map (mini map) repositions the main map such that the area clicked is centred on the viewport.

Clicking or dragging the compass face rotates the map.

Predefined Views

GenGIS also provides predefined Perspective and Top views.

To quickly switch to a perspective view or a top down view use either the corresponding toolbar buttons (left) or the menu options located in the View → Camera Position.

Layer Tree Controller

The Layer Tree Controller (Windows)

The Layer Tree Controller is located in a left panel within GenGIS and provides a hierarchical view of the Study, Map, Location Set, Location, Sequence and Tree layers.

Double clicking on the title of any layer within the controller (or right-clicking the same region and selecting Properties from a pop-up menu) opens a corresponding properties dialog for that layer.

Layers can be enabled (shown) and disabled (hidden) by clicking on corresponding 'x' control boxes within the controller.

Location Legend

The Location Legend (Windows)

The Location Legend is located in a left panel within GenGIS and provides an overview of colour, shape and size selections for locations.

Left clicking on a colour, shape or size opens a properties dialog to modify that particular field.

Sequence Legend

The Sequence Legend (Windows)

The Sequence Legend is located in a left panel within GenGIS and provides an overview of different available sequence fields.

A sequence colour can be modified by clicking on its colour button within the Sequence Legend panel.

Console Panels

GenGIS features an output console and a Python console both located at the bottom of the main interface.

Output Console

The Output Console displays a log of successful program operations (e.g., loading data files such as map files) as well as possible errors.

The GenGIS console.

Python Console

The Python console contains a fully-functional Python interpreter that provides access to data structures within GenGIS (e.g., location layer data) and API functions (e.g., the ability to automate camera and lighting controls via Python scripting). The Python console is described in greater detail later in the manual.

The GenGIS Python console.

Interacting with sample sites

Layer Property Dialogs

Study Layer Properties

The Study Layer is automatically created during a new session. The Study Properties dialog provides controls to change settings such as study layer metadata (name, description and authors), background colour and terrain resolution. Components of the Study Layer properties dialog are explained in greater detail below.

The Number Entries controller specifies the number of distinct colour layers.

Individual colours and their corresponding elevation can be adjusted in the nested window containing colour buttons.

Colour-to-elevation representation can be evenly distributed by clicking the Evenly space entries button.

Symbology > Advanced Tab

Display properties such as vertical exaggeration, level of map detail and transparency can be adjusted within the Advanced tab.

A wireframe mode checkbox displays the map as a transparent wireframe.

Metadata Tab

Metadata from the map file (e.g., dimensions, origin) are visible within the Metadata tab.

Vector Map Layer Properties

The Vector Map Layer displays a shapefile. One or more than one Shapefiles can be loaded and visuialized in GenGIS. The Vector Map Layer properties dialog controls settings such as vector map layer metadata (e.g., name, description) and visual properties for shapefile features. Metadata for each shapefile (e.g., projection, number of features,...) is also organized and displayed. Components of the Vector Map Layer properties dialog are explained in greater detail below.

General Tab

The General tab contains three editable layer metadata fields: Layer name, Description, and Authors. Changing the layer name also changes the name of the layer within the Layer Tree Controller.

Symbology > Point Tab

The Point tab provides controls to change the size, shape, border colour, filling colour, and border size of point features.

Symbology > Polyline Tab

The Polyline tab provides controls to change the line style, colour, thickness, border size, and border colour of line features.

Symbology > Polygon Tab

The Polygon tab provides controls to change the style, thickness, and colour for the border line of polygon features.

Metadata Tab

Metadata from the shapefile (e.g., projection, features type) are visible within the Metadata tab.

Location Set Layer Properties

A location file is treated as a location set layer containing several distinct location layers. The Location Set Layer properties dialog controls settings such as location set layer metadata (e.g., name, description) and visual properties for both locations and charts (e.g., colour, size). Metadata from the location file (e.g., number of sites) is also displayed. At this time, GenGIS supports a single location file per session. Components of the Location Set Layer properties dialog are explained in greater detail below.

General Tab

The General tab contains three editable layer metadata fields: Layer name, Description, and Authors. Changing the layer name also changes the name of the layer within the Layer Tree Controller.

Location Set > Colour Tab

The colour tab provides controls to modify location colour.

All locations can be displayed in a uniform colour by selecting the Uniform colour check-box.

Alternatively, each location can assigned a unique colour based on a property (e.g., environment type). This is performed by un-selecting the Uniform colour check-box and selecting appropriate Field to char and Colour map fields.

Individual colours for locations can be adjusted in the nested window containing rows of colour buttons.

Controls to modify location border colour and width are also provided.

Location Set > Shape Tab

The shape tab provides controls to modify location shape.

All locations can be displayed in a uniform shape by selecting the Uniform shape check-box.

Alternatively, each location can assigned a unique shape based on a property (e.g., environment type). This is performed by un-selecting the Uniform shape check-box and selecting appropriate Field to char and Shape map fields.

Individual shapes for locations can be adjusted in the nested window containing rows of shape selection menus.

Location Set > Size Tab

The size tab provides controls to modify location size.

Each location can assigned a unique size based on a numeric property (e.g., easting). This is performed by selecting a value from Field to chart and assigning distinct minimum and maximum values.

Location Set > Label Tab

Visibility and properties of labels stored in location files can be configured from within the Label tab.

If location charts are enabled, labels can be bound to the charts by selecting the Bind labels to charts check-box.

The General tab contains three editable layer metadata fields: Layer name, Description, and Authors. Changing the layer name also changes the name of the layer within the Layer Tree Controller.

Metadata Tab

Metadata from the sequence file (e.g., division) is visible within the Metadata tab.

Tree Layer Properties

GenGIS supports 2D and 3D trees (e.g., phylogenetic or hierarchical cluster tree). Different display properties (e.g., colour, line width) can be assigned to trees through the Tree Layer Properties dialog. GenGIS supports loading multiple trees during a single session. Components of the Tree Layer properties dialog are explained in greater detail below.

General Tab

The General tab contains three editable layer metadata fields: Layer name, Description, and Authors. Changing the layer name also changes the name of the layer within the Layer Tree Controller.

Symbology > Tree Tab

Tree layout and style properties can be set from within the Tree tab.

Symbology > Connecting Lines Tab

Location, correlation and 3D drop line properties can be set from within the Connecting Lines tab.

Symbology > Geography Line Tab

Geography line and geographic point properties can be set from within the Geography Line tab.

Label Tab

Tree label size, colour and visibility can be set from within the Label tab.

Metadata Tab

Metadata from the tree file (e.g., number of nodes) is visible within the Metadata tab.

Graphical analysis tools in GenGIS

Basic data visualizations

GenGIS provides a number of ways to visualize data. Chief among these are visualizing summaries of sequence data as charts, and visualizing the relationship between location specific data as 2D or 3D trees. Other visualization are implemented as plugins and custom visualization can be generated through the Python interface.

Visualizing sequence data as charts

GenGIS supports both bar charts and pie charts to represent sequence data within locations. Charts are configured through Chart tab of the Location Set Layer Properties dialog. The sequence metadata field to graph is set through the Field to chart combobox. The colour assigned to each field element depends on the selected colour map and can be customized as desired. If your Sequence File contains a field indicating the number of times each sequence type was identified at a given location this can be set through the Create quantitative charts using count data in field combobox. By enabling or disabling this feature, qualitative (richness) and quantitative (evenness) pie charts can easily be created. The Symbology tab allows one to specify the type of chart to create and to set properties effecting the appearance of charts. In particular, the size of charts can be set to reflect the number of sequences obtained at a location by enabling the Set chart size proportional to number of sequences checkbox. For pie charts, the abundance at which sequence types (e.g., taxa) are assigned to the Other category is set through the Assign taxa to other field.

Charts > Colour Map Tab

Charts > Symbology (1) Tab (Chart type: Bar Chart)

Charts > Symbology (2) Tab (Chart type: Pie Chart)

3D Trees

Trees in Newick file format can be loaded into GenGIS. Leaf nodes within a tree must match up with either a Site ID from the location file or a Sequence ID from the sequence file. By default, trees are shown as 3D geophylogenies:

2D and 3D geophylogeny of Banza katydids from the Hawaiian Islands (data by Shapiro et al.)

The visual properties of 3D trees are highly customizable and can be modified through the Tree Layer Properties dialog.

2D Trees

GenGIS supports the quantitative visualization of 2D trees which can be used as an exploratory tool. Specifically, users can define a geographic axis and visualize how well the topology of a tree correlates with the ordering of geographic locations along this axis. This is accomplished by finding the ordering of leaf nodes, subject to the constraints of the tree topology, which minimizes the number of crossings that occur between lines that connect leaf nodes to their associated geographic locations. In this optimal layout, the number of crossings that occur between these lines is a quantitative measure of the amount of discordance which exists between the topology of the tree and the user defined geographic axis. Further information about this quantitative 2D visualization technique can be found in:

Defining axes

To generate a 2D tree, a Layout Line must first be drawn. Select the Layout Line from the main toolbar, click on the map where you would like the line to start, and then click again where you would like the line to end. The 2D tree will always be drawn on the right-hand side of the Layout Line as you walk from the start to the end of the line. To generate a 2D tree, right-click on the Tree Layer in the Layer Tree and select 2D slanted cladogram, 2D cladogram, or 2D phylogram from the pop-up menu.

If you wish to specify a non-linear geographic axes, select Draw geographic axis from the main toolbar. You can now draw a polyline within the Viewport by clicking on the desired start and end points of individual line segments. Press Enter when you are finished drawing the polyline. You can right-click on any polyline vertex and select Extend geographic axis to draw more complicated non-linear axes. Note that only locations which reside close to the specified polyline are considered and all other locations are projected out of the tree.

Draw layout line

Draw a straight line which can be used to layout graphic elements such as a 2D tree or pie charts.

Draw geographic axis

Draw a polyline which can be used to test the goodness-of-fit between a tree and a non-linear geographic axes (see 2D Pylogenetic Trees).

Manipulation

The geographic axis being evaluated can be modified dynamically. To modify the geographic axis, simple click on either of the end-points of the Layout Line and drag it to a new location. The vertices defining a non-linear geographic axes can also be modified dynamically. Making the Layout Line shorter will reduce the size of the 2D tree. The height of the tree can also be modified in the Tree Layer Properties dialog. You can also drag the root node of a tree to re-position the tree while keeping the Layout Line at the same orientation.

Visual Properties

The visual properties of 2D trees are highly customizable and can be modified through the Tree Layer Properties dialog.

Statistical Test

A Monte Carlo permutation test can be used to test whether or not the fit of ordered leaf nodes to geographic points is significantly better than expected by chance alone. This null hypothesis is tested by holding the tree topology, geographic axis, and the association between leaf nodes and geographic locations constant while permuting the ordering of geographic locations along the geographic layout line. After each random permutation, the new optimal ordering of leaf nodes is determined and the number of edge crossings is determined. By generating many random permutations, we obtain an estimate of the probability mass function of the null model. The reported p-value is the fraction of permutations that have a number of crossings fewer than or equal to the number of crossings in the original model. Note: this explanation differs slights from the one given in Parks and Beiko, 2009 where the association between leaf nodes and geographic locations was permuted. In practice, this results in the same null distribution though special care must be taken to properly handle geographic locations which are associated with multiple leaf nodes.

To perform a Monte Carlo permutation test, right-click on the Tree Layer in the Layer Tree and select Perform significant test (on full tree) from the pop-up menu. The permutation test can also be applied to any subtree by right clicking on the root node of the subtree and selecting Perform significant test on subtree from the pop-up menu. The results of the permutation test are shown as a graph which indicates the calculated p-value along with the estimated probability density function. The number of crossings occuring on the actual data is shown by a red line.

Plot showing results of a Monte Carlo permutation test.

Linear Axes Analysis

GenGIS allows the number of crossing which occur for all linear gradients to be explored. Right-click on the subtree of the geophylogeny you wish to analyze and select Perform linear axis analysis on subtree. This will produce a graph showing the number of crossings which occur for all possible linear gradients. Clicking on the graph causes the linear layout line to rotate to a given orientation. Running a permutation test causes a red line to be drawn on the plot which indicates the number of crossings at which the specified critical value (i.e., p-value = 0.05) is obtained. That is, linear gradients with orientations resulting in fewer crossings are significant at the selected p-value.

Graph showing the number of crossings for all possible linear gradients.

The Python console and API functions

What you can do with the console

The Python Console provides access to a standard Python interpreter. Python is a general-purpose high-level programming language with many packages available for phylogenetics, population genetics, and statistics. Data loaded into GenGIS is exposed to the Python Console allowing quanitative hypothesis testing to be performed directly within GenGIS. Results of analyses can be visualized within the Viewport to aid in interpretation of results and generation of new hypotheses.

Below we give several short examples of using this API. You can also find information about using the API on our tutorials page.

Filtering data

We have provided a simple function, filterData, for filtering data. This function is contained in dataHelper.py. As an example, all locations with a temperature greater than 20 can be obtained as follows:

Basic filtering functions are provided in filterFunc.py, but it is easy to write your own filtering functions. For example, the equal filter used above is simply:

def equal(val1, val2):
return str(val1) == str(val2)

Creating custom data visualizations

Using the VisualLine, VisualMarker, and VisualLabel classes one can create custom data visualizations with GenGIS. The VisualLine class allows user defined lines to be drawn in the Viewport. Suppose we have two locations within our location set with ids of 'GBR' and 'ITA'. We can draw a line between these locations as follows:

# draw a solid red line with a width of 2 between these countries
line = GenGIS.VisualLine(GenGIS.Colour(1,0,0), 2, GenGIS.LINE_STYLE.SOLID, GenGIS.Line3D(gbrPt, itaPt))
lineId = GenGIS.graphics.AddLine(line)
GenGIS.viewport.Refresh()

The visual properties of this line can easily be changed at any time to reflect different aspects of your data:

The VisualMarker class allows user defined markers to be drawn in the Viewport. It is similar to the VisualLine class. For example, we can draw a blue circle over London which is situated at a longitude 0.128W and a latitude of 51.51N as follows:

VisualLabels can be used to create orthographic (e.g., to indicate a legend or figure caption) or perspective text (e.g., to label points on a map). We can create a "Hello World!" label for a map as follows:

By combining these graphical primative and encoding key aspects of your data to different visual properties (i.e., colour, size, shape) GenGIS can be used to identify interesting patterns within a wide-range of datasets. An example which uses these classes to visualizing a distance matrix indicating the rate of import and export of HIV-1 subtype B for different European countries as reported by Paraskevis et al. (2009) is available here.

Creating fly-through movies

A collection of functions for creating fly-through movies are available in movieHelper.py found in the scripts directory. A useful movie is to rotate the map about its origin. Such a movie can be made using the rotateAboutOrigin function which takes the number of degrees to rotate and the time of the movie as parameters:

import movieHelper
movieHelper.rotateAboutOrigin(360, 10)

More general movies can be created by capturing the camera parameters at key frames using the function getCameraParam and then interpolating between these key frames using the function linearInterpolateParams:

import movieHelper
# move camera to first key frame (for example, use the toolbar to set a top down view)
keyFrame1 = movieHelper.getCameraParam()
# move camera to next key frame (for example, use the toolbar to set the default perspective view)
keyFrame2 = movieHelper.getCameraParam()
# set camera back to first key frame
movieHelper.setCameraParam(keyFrame1)
# smoothly move between these key frames in 5 seconds
movieHelper.linearInterpolateParams(keyFrame1, keyFrame2, 5)

For examples of creating custom movies which do not use the movieHelper API, have a look at the series of H1N1 movies we have developed. In particular, note that GenGIS.mainWindow.Yield() must be called occasionally for time series to run correctly.

By stitching together multiple key frames complex fly-through movies can be created. Commercial software such as Camtasia or open source software such as CamStudio can be used to record these movies.

RPy and analyzing data

GenGIS makes use of the [RPy2 libraries which allow R commands to be embedded in Python. If you are familiar with R, then the key to operating at the interface of GenGIS, Python and R is understanding how to ensure data are in the right scope.

Important: GenGIS is built with a version of RPy2 (2.03) that is quite a bit older than the current release. This should not prevent you from doing analyses with RPy2, but it does mean that the current RPy2 documentation is not relevant. We recommend referring to documentation in the 2.0 series, for instance the [Version 2.08 documentation].

Data managed by GenGIS need to be retrieved into the Python environment using the GenGIS API functions.

Data in the Python environment need to be passed to R in one of two ways by passing the Python data structure to R either before the desired analysis is invoked, or at the time of invocation. The choice of approach depends on what the R call is looking for: in general it is less elegant but easier to set everything in advance.

More-detailed examples of how to do this are shown in the tutorials, and plugins such as the Mantel test that use R can be mined for additional working examples.

The first step is to import RPy2 and set up a shortcut for invoking R commands. This is accomplished with the following commands:

import rpy2
import rpy2.robjects as robjects
r = robjects.r

If this works, then any R command can be invoked using the syntax r("command"). It is important to remember, though, that everything inside the quotation marks needs to be in R's scope.

Here is the general procedure to follow for getting data from Python into R:

First, create the Python data structure. For example, if the ultimate goal is an R vector, then you can start out with a Python list:

pyList = [1,2,2,3,3,4,4,4,4,5,5,5,6,6,6,6,6,7,8,8,9,10,10]

Second, use rpy2 to create an R data structure that is visible in Python (but not yet in R!).

rVecInPy = r["c"](robjects.IntVector(pyList))

This uses the R command c() to create an integer vector. We now have an R data structure, but R can't see it yet!

Third, create a version of the data structure in the R environment. We do this by setting values in robjects.globalEnv:

robjects.globalEnv["rVecInR"] = rVecInPy

Now we have a copy of the R array in the R environment, so we can use the variable embedded within quotation marks in an r("") command:

r("hist(rVecInR)")

This will create a frequency histogram using the default parameters. Any parameters of hist() can be set inside the double quotes as they would be in a native R environment.